R2DT: a comprehensive platform for visualizing RNA secondary structure

Holly McCann(Georgia Institute of Technology), Caeden D. Meade(Georgia Institute of Technology), Loren Dean Williams(Georgia Institute of Technology), Anton S. Petrov(Georgia Institute of Technology), Philip Z. Johnson(University of Maryland, College Park), Anne E. Simon(University of Maryland, College Park), David Hoksza(Charles University), Eric P. Nawrocki(National Institutes of Health), Patricia P. Chan(University of California, Santa Cruz), Todd M. Lowe(University of California, Santa Cruz), Carlos Eduardo Ribas(European Bioinformatics Institute), Blake Sweeney(European Bioinformatics Institute), Fábio Madeira(European Bioinformatics Institute), Stephen Anyango(European Bioinformatics Institute), Sri Devan Appasamy(European Bioinformatics Institute), Mandar Deshpande(European Bioinformatics Institute), Mihály Váradi(European Bioinformatics Institute), Sameer Velankar(European Bioinformatics Institute), Craig L. Zirbel(Bowling Green State University), Aleksei Naiden(Oldham Council), Fabrice Jossinet(Université de Strasbourg), Anton I. Petrov(Georgia Institute of Technology)
Nucleic Acids Research
February 8, 2025
10.1093/nar/gkaf032
Cited by 22Open Access
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Abstract

RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.

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